Isla ArenaC O N S U L T I N G
Volunteer OpportunitiesWe welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact UsProject Manager Marilyn Latta mlattascccagov 510-286-4157Science Lead Katharyn Boyer katboyersfsuedu 415-338-3751
This document was produced for the State Coastal Conservancyby ESA PWA 2012
Photo creditsLorenz amp Avelar wwwLorenz-AvelarcomSan Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab)Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte)USGS (Susan de la Cruz)ESA PWA (Doug George)
Literature Cited1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
12
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San RafaelBay
HaywardShoreline
ProjectDevelopment
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Isla ArenaC O N S U L T I N G
12
other restoration efforts in the estuary and around the nation The pilot project will be conducted in two
recommends the use of Living Shorelines as a potential
M A Y 2 0 1 2
The San Francisco Bay Living ShorelinesNearshore Linkages Project
be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
Coastal Conservancy Climate Change Policy also recommends
locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will functions and values The State
adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat
Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
Living Shorelines and Climate Change Adaptation The California Climate Change Adaptation Strategy
What is a Living Shoreline Living Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
11
Partners
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAAFisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
Permitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
Ecological EngineersEelgrass and Native Oysters
Eelgrass Eelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
Native Oysters Native oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Connecting the PiecesSan Francisco BaySubtidal Habitat Goals
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh
subtidal integration and living shorelines and in what quantities 2 Develop best practices for integrating subtidal restoration
with adjacent wetlands 3 Develop best practices for pilot projects to create living
shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay 2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay 3 Explore the use of living shoreline projects as a way to
achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
2
The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
- Native oysters will recruit with densities of gt10000 oysters per acre of substrate
- Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction
- The number of visits by fish species to the larger scale project will increase by 50 relative to pre-construction visits and the large control area with no physical structure
- Eelgrass will establish and spread to at least twice initial planting densities
Success Criteria
10
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Living Shorelines inSan Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on
_ eelgrass and oyster reefs began in 2004 Several small-scale
_ Hayward Shoreline Site^ subtidal eelgrass restoration projects were established_ San Rafael Bay Site^ coupled with extensive monitoring and genetics analysis
Native Oysters Eelgrass from seven eelgrass beds in the bay Native oyster monitor-
ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and_
planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely
acute designed San Francisco Bay Living Shorelines6 0 63 km
Overarching Project GoalTo create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
Objectives to Achieve Goal
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Ba y 2 Compare the ef fectiveness of different restoration treatments in establishing these habitat-forming species 3 Determine the extent to which restoration treatments enhance habitat for
invertebrates fish and birds relative to areas lacking structure and
pre-treatment conditions 4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or
combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) dif
ferently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of
nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats 6 Evaluate potential for living subtidal features to reduce water flow velocities
attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently
7 Determine if position in the Bay and the specific environmental context at that location influences foundational species
establishment habitat provision and physical processes conferred by restoration treatments 8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along
mudflatswetlands versus armored shores 3
Whalersquos Tail Marsh (North)
(ELER)
Mudflat
SF Bay
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
to Mt Eden Creek
Pond E10Levee
Mudflat
SF Bay
to Mt Eden Creek
Shell bag mounds
Eelgrassvegetative shoots
Shell bag mound + eelgrassShell bag mound
Eelgrass
Control
~250 m
Shell bag mound + eelgrass
Eelgrass
Shell bag mound
Layer cake
4m
1m
2 m2 m
1 m1 m
Reef castle
Reef ball
Reef ball stack
Hayward Shoreline Location Experiment Details
Proposed Array of Treatments at Hayward Shoreline
9
Hayward Shoreline North
Hayward Shoreline South
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Phase 1 detailSubstrate experiment40 m x 1 m
Phase 2 detailLarger scale experiment32 m x 10 mShell bag mound + eelgrass
cement These oyster substrates will also be placed onto coir The Project Elements fabric This design should reduce settlement into the sediment and scour around the treatments experienced in
Eelgrass Units Eelgrass shoots transplantsEelgrass will be planted and
seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-
Buoy-deployed seedingment transplants and increase of eelgrass
genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate Units Each oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag Mounds Bags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
previous projects
Dome Style Reef Balls Reef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball Stacks Reef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer Cakes The Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef Castles Reef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
4
s
acute0 100 20050
Meters
Substrate Elements at Hayward Shoreline NorthC r o s s S e c t i o n
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
MHHW
MLLW
Mudflat
~ 250 m1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound+ eelgrass
Eelgrass Shell bag mound Layer cake Reef castle Reef ballReef ball stack
1m 1m
8
Highest priority To achieve if possible
Appropriate region and depth for eelgrass and oysters
Large enough shoreline oriented so that treatment array can be placed parallel to the shore and perpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison of treatment effects in different regions
Appropriate sediment for oyster reefs and eelgrass
Distance to shore amenable to shore access for ease of monitoring
Same experimental design and depth if mulƟple locaƟons
SoŌ shoreline with paired comparison to hard shoreline nearby if possible
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale Experiment The larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Site Selection Criteria
ELEMENT
UNIT
PLOT
SITE
LOCATION
Project Components
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with
reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
Substrate Experiment The substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Very important
Willing landowners with expected reasonable Ɵme frame for permits approvals
5
DetailLarger scale experiment32 m x 10 m
Proposed Array of Treatments at San Rafael BayP h a s e 1
DetailSubstrate experiment30 m x 1 m
7
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
SF Bay
Lagoon
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Mudflat
Shell bag mounds
Eelgrass vegetative shoots
2 m2 m
1 m1 m
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
S
San Rafael Canal
Location 1 San Rafael Bay
San Rafael Bay lies between Point San site from direct wave action from the Quentin to the south and Point San east out of the more exposed portions Su ments
Tre tsPedro to the north and is a wide of San Pablo Bay The shoreline near shallow mudflat This mud which was the project site is also affected by ship deposited in the 1800s during the boat and seaplane landing wakes hydraulic mining period is slowly degrading and appears to be approach- The project location allows the experi-ing conditions prior to mining ments to be conducted near an armored
shoreline Native oysters are abundant The San Rafael Bay project location is on the lower rip-rap along the shoreline in a coastal area owned by The Nature and eelgrass test plots have been Conservancy and is subject to the successful on this property over the last mixed semi-diurnal tides typical to San 4 years Both eelgrass and native Francisco Bay The east-southeast oysters have been successfully restored orientation of San Rafael Bay provides nearby at the Marin Rod and Gun Club protection from the easterly summer sea Herring often spawn along this shore-breezes and exposure to the southeast- line and should benefit from restored erly winter storms The Marin Islands subtidal habitat National Wildlife Refuge protects the acute
0 50 100 200 Meters
Substrate Elements at San Rafael Bay Substrate Elements at San Rafael BayCross Section C r o s s S e c t i o n
1 m ~ 250 m
MHHW
MLLW
SF Bay Mudflat Lagoon
~1m~1m
1m
Layer cake
Schematic representation not to exact scale
Note
1m
Reef ball stack
1m
Reef castle
1m
Reef ball
6
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
11
Partners
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAAFisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
Permitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
Ecological EngineersEelgrass and Native Oysters
Eelgrass Eelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
Native Oysters Native oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Connecting the PiecesSan Francisco BaySubtidal Habitat Goals
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh
subtidal integration and living shorelines and in what quantities 2 Develop best practices for integrating subtidal restoration
with adjacent wetlands 3 Develop best practices for pilot projects to create living
shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay 2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay 3 Explore the use of living shoreline projects as a way to
achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
2
The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
- Native oysters will recruit with densities of gt10000 oysters per acre of substrate
- Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction
- The number of visits by fish species to the larger scale project will increase by 50 relative to pre-construction visits and the large control area with no physical structure
- Eelgrass will establish and spread to at least twice initial planting densities
Success Criteria
10
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Living Shorelines inSan Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on
_ eelgrass and oyster reefs began in 2004 Several small-scale
_ Hayward Shoreline Site^ subtidal eelgrass restoration projects were established_ San Rafael Bay Site^ coupled with extensive monitoring and genetics analysis
Native Oysters Eelgrass from seven eelgrass beds in the bay Native oyster monitor-
ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and_
planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely
acute designed San Francisco Bay Living Shorelines6 0 63 km
Overarching Project GoalTo create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
Objectives to Achieve Goal
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Ba y 2 Compare the ef fectiveness of different restoration treatments in establishing these habitat-forming species 3 Determine the extent to which restoration treatments enhance habitat for
invertebrates fish and birds relative to areas lacking structure and
pre-treatment conditions 4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or
combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) dif
ferently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of
nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats 6 Evaluate potential for living subtidal features to reduce water flow velocities
attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently
7 Determine if position in the Bay and the specific environmental context at that location influences foundational species
establishment habitat provision and physical processes conferred by restoration treatments 8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along
mudflatswetlands versus armored shores 3
Whalersquos Tail Marsh (North)
(ELER)
Mudflat
SF Bay
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
to Mt Eden Creek
Pond E10Levee
Mudflat
SF Bay
to Mt Eden Creek
Shell bag mounds
Eelgrassvegetative shoots
Shell bag mound + eelgrassShell bag mound
Eelgrass
Control
~250 m
Shell bag mound + eelgrass
Eelgrass
Shell bag mound
Layer cake
4m
1m
2 m2 m
1 m1 m
Reef castle
Reef ball
Reef ball stack
Hayward Shoreline Location Experiment Details
Proposed Array of Treatments at Hayward Shoreline
9
Hayward Shoreline North
Hayward Shoreline South
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Phase 1 detailSubstrate experiment40 m x 1 m
Phase 2 detailLarger scale experiment32 m x 10 mShell bag mound + eelgrass
cement These oyster substrates will also be placed onto coir The Project Elements fabric This design should reduce settlement into the sediment and scour around the treatments experienced in
Eelgrass Units Eelgrass shoots transplantsEelgrass will be planted and
seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-
Buoy-deployed seedingment transplants and increase of eelgrass
genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate Units Each oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag Mounds Bags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
previous projects
Dome Style Reef Balls Reef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball Stacks Reef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer Cakes The Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef Castles Reef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
4
s
acute0 100 20050
Meters
Substrate Elements at Hayward Shoreline NorthC r o s s S e c t i o n
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
MHHW
MLLW
Mudflat
~ 250 m1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound+ eelgrass
Eelgrass Shell bag mound Layer cake Reef castle Reef ballReef ball stack
1m 1m
8
Highest priority To achieve if possible
Appropriate region and depth for eelgrass and oysters
Large enough shoreline oriented so that treatment array can be placed parallel to the shore and perpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison of treatment effects in different regions
Appropriate sediment for oyster reefs and eelgrass
Distance to shore amenable to shore access for ease of monitoring
Same experimental design and depth if mulƟple locaƟons
SoŌ shoreline with paired comparison to hard shoreline nearby if possible
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale Experiment The larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Site Selection Criteria
ELEMENT
UNIT
PLOT
SITE
LOCATION
Project Components
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with
reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
Substrate Experiment The substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Very important
Willing landowners with expected reasonable Ɵme frame for permits approvals
5
DetailLarger scale experiment32 m x 10 m
Proposed Array of Treatments at San Rafael BayP h a s e 1
DetailSubstrate experiment30 m x 1 m
7
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
SF Bay
Lagoon
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Mudflat
Shell bag mounds
Eelgrass vegetative shoots
2 m2 m
1 m1 m
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
S
San Rafael Canal
Location 1 San Rafael Bay
San Rafael Bay lies between Point San site from direct wave action from the Quentin to the south and Point San east out of the more exposed portions Su ments
Tre tsPedro to the north and is a wide of San Pablo Bay The shoreline near shallow mudflat This mud which was the project site is also affected by ship deposited in the 1800s during the boat and seaplane landing wakes hydraulic mining period is slowly degrading and appears to be approach- The project location allows the experi-ing conditions prior to mining ments to be conducted near an armored
shoreline Native oysters are abundant The San Rafael Bay project location is on the lower rip-rap along the shoreline in a coastal area owned by The Nature and eelgrass test plots have been Conservancy and is subject to the successful on this property over the last mixed semi-diurnal tides typical to San 4 years Both eelgrass and native Francisco Bay The east-southeast oysters have been successfully restored orientation of San Rafael Bay provides nearby at the Marin Rod and Gun Club protection from the easterly summer sea Herring often spawn along this shore-breezes and exposure to the southeast- line and should benefit from restored erly winter storms The Marin Islands subtidal habitat National Wildlife Refuge protects the acute
0 50 100 200 Meters
Substrate Elements at San Rafael Bay Substrate Elements at San Rafael BayCross Section C r o s s S e c t i o n
1 m ~ 250 m
MHHW
MLLW
SF Bay Mudflat Lagoon
~1m~1m
1m
Layer cake
Schematic representation not to exact scale
Note
1m
Reef ball stack
1m
Reef castle
1m
Reef ball
6
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
- Native oysters will recruit with densities of gt10000 oysters per acre of substrate
- Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction
- The number of visits by fish species to the larger scale project will increase by 50 relative to pre-construction visits and the large control area with no physical structure
- Eelgrass will establish and spread to at least twice initial planting densities
Success Criteria
10
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Living Shorelines inSan Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on
_ eelgrass and oyster reefs began in 2004 Several small-scale
_ Hayward Shoreline Site^ subtidal eelgrass restoration projects were established_ San Rafael Bay Site^ coupled with extensive monitoring and genetics analysis
Native Oysters Eelgrass from seven eelgrass beds in the bay Native oyster monitor-
ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and_
planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely
acute designed San Francisco Bay Living Shorelines6 0 63 km
Overarching Project GoalTo create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
Objectives to Achieve Goal
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Ba y 2 Compare the ef fectiveness of different restoration treatments in establishing these habitat-forming species 3 Determine the extent to which restoration treatments enhance habitat for
invertebrates fish and birds relative to areas lacking structure and
pre-treatment conditions 4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or
combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) dif
ferently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of
nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats 6 Evaluate potential for living subtidal features to reduce water flow velocities
attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently
7 Determine if position in the Bay and the specific environmental context at that location influences foundational species
establishment habitat provision and physical processes conferred by restoration treatments 8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along
mudflatswetlands versus armored shores 3
Whalersquos Tail Marsh (North)
(ELER)
Mudflat
SF Bay
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
to Mt Eden Creek
Pond E10Levee
Mudflat
SF Bay
to Mt Eden Creek
Shell bag mounds
Eelgrassvegetative shoots
Shell bag mound + eelgrassShell bag mound
Eelgrass
Control
~250 m
Shell bag mound + eelgrass
Eelgrass
Shell bag mound
Layer cake
4m
1m
2 m2 m
1 m1 m
Reef castle
Reef ball
Reef ball stack
Hayward Shoreline Location Experiment Details
Proposed Array of Treatments at Hayward Shoreline
9
Hayward Shoreline North
Hayward Shoreline South
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Phase 1 detailSubstrate experiment40 m x 1 m
Phase 2 detailLarger scale experiment32 m x 10 mShell bag mound + eelgrass
cement These oyster substrates will also be placed onto coir The Project Elements fabric This design should reduce settlement into the sediment and scour around the treatments experienced in
Eelgrass Units Eelgrass shoots transplantsEelgrass will be planted and
seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-
Buoy-deployed seedingment transplants and increase of eelgrass
genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate Units Each oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag Mounds Bags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
previous projects
Dome Style Reef Balls Reef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball Stacks Reef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer Cakes The Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef Castles Reef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
4
s
acute0 100 20050
Meters
Substrate Elements at Hayward Shoreline NorthC r o s s S e c t i o n
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
MHHW
MLLW
Mudflat
~ 250 m1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound+ eelgrass
Eelgrass Shell bag mound Layer cake Reef castle Reef ballReef ball stack
1m 1m
8
Highest priority To achieve if possible
Appropriate region and depth for eelgrass and oysters
Large enough shoreline oriented so that treatment array can be placed parallel to the shore and perpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison of treatment effects in different regions
Appropriate sediment for oyster reefs and eelgrass
Distance to shore amenable to shore access for ease of monitoring
Same experimental design and depth if mulƟple locaƟons
SoŌ shoreline with paired comparison to hard shoreline nearby if possible
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale Experiment The larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Site Selection Criteria
ELEMENT
UNIT
PLOT
SITE
LOCATION
Project Components
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with
reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
Substrate Experiment The substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Very important
Willing landowners with expected reasonable Ɵme frame for permits approvals
5
DetailLarger scale experiment32 m x 10 m
Proposed Array of Treatments at San Rafael BayP h a s e 1
DetailSubstrate experiment30 m x 1 m
7
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
SF Bay
Lagoon
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Mudflat
Shell bag mounds
Eelgrass vegetative shoots
2 m2 m
1 m1 m
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
S
San Rafael Canal
Location 1 San Rafael Bay
San Rafael Bay lies between Point San site from direct wave action from the Quentin to the south and Point San east out of the more exposed portions Su ments
Tre tsPedro to the north and is a wide of San Pablo Bay The shoreline near shallow mudflat This mud which was the project site is also affected by ship deposited in the 1800s during the boat and seaplane landing wakes hydraulic mining period is slowly degrading and appears to be approach- The project location allows the experi-ing conditions prior to mining ments to be conducted near an armored
shoreline Native oysters are abundant The San Rafael Bay project location is on the lower rip-rap along the shoreline in a coastal area owned by The Nature and eelgrass test plots have been Conservancy and is subject to the successful on this property over the last mixed semi-diurnal tides typical to San 4 years Both eelgrass and native Francisco Bay The east-southeast oysters have been successfully restored orientation of San Rafael Bay provides nearby at the Marin Rod and Gun Club protection from the easterly summer sea Herring often spawn along this shore-breezes and exposure to the southeast- line and should benefit from restored erly winter storms The Marin Islands subtidal habitat National Wildlife Refuge protects the acute
0 50 100 200 Meters
Substrate Elements at San Rafael Bay Substrate Elements at San Rafael BayCross Section C r o s s S e c t i o n
1 m ~ 250 m
MHHW
MLLW
SF Bay Mudflat Lagoon
~1m~1m
1m
Layer cake
Schematic representation not to exact scale
Note
1m
Reef ball stack
1m
Reef castle
1m
Reef ball
6
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
Whalersquos Tail Marsh (North)
(ELER)
Mudflat
SF Bay
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
to Mt Eden Creek
Pond E10Levee
Mudflat
SF Bay
to Mt Eden Creek
Shell bag mounds
Eelgrassvegetative shoots
Shell bag mound + eelgrassShell bag mound
Eelgrass
Control
~250 m
Shell bag mound + eelgrass
Eelgrass
Shell bag mound
Layer cake
4m
1m
2 m2 m
1 m1 m
Reef castle
Reef ball
Reef ball stack
Hayward Shoreline Location Experiment Details
Proposed Array of Treatments at Hayward Shoreline
9
Hayward Shoreline North
Hayward Shoreline South
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Phase 1 detailSubstrate experiment40 m x 1 m
Phase 2 detailLarger scale experiment32 m x 10 mShell bag mound + eelgrass
cement These oyster substrates will also be placed onto coir The Project Elements fabric This design should reduce settlement into the sediment and scour around the treatments experienced in
Eelgrass Units Eelgrass shoots transplantsEelgrass will be planted and
seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-
Buoy-deployed seedingment transplants and increase of eelgrass
genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate Units Each oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag Mounds Bags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
previous projects
Dome Style Reef Balls Reef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball Stacks Reef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer Cakes The Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef Castles Reef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
4
s
acute0 100 20050
Meters
Substrate Elements at Hayward Shoreline NorthC r o s s S e c t i o n
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
MHHW
MLLW
Mudflat
~ 250 m1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound+ eelgrass
Eelgrass Shell bag mound Layer cake Reef castle Reef ballReef ball stack
1m 1m
8
Highest priority To achieve if possible
Appropriate region and depth for eelgrass and oysters
Large enough shoreline oriented so that treatment array can be placed parallel to the shore and perpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison of treatment effects in different regions
Appropriate sediment for oyster reefs and eelgrass
Distance to shore amenable to shore access for ease of monitoring
Same experimental design and depth if mulƟple locaƟons
SoŌ shoreline with paired comparison to hard shoreline nearby if possible
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale Experiment The larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Site Selection Criteria
ELEMENT
UNIT
PLOT
SITE
LOCATION
Project Components
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with
reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
Substrate Experiment The substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Very important
Willing landowners with expected reasonable Ɵme frame for permits approvals
5
DetailLarger scale experiment32 m x 10 m
Proposed Array of Treatments at San Rafael BayP h a s e 1
DetailSubstrate experiment30 m x 1 m
7
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
SF Bay
Lagoon
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Mudflat
Shell bag mounds
Eelgrass vegetative shoots
2 m2 m
1 m1 m
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
S
San Rafael Canal
Location 1 San Rafael Bay
San Rafael Bay lies between Point San site from direct wave action from the Quentin to the south and Point San east out of the more exposed portions Su ments
Tre tsPedro to the north and is a wide of San Pablo Bay The shoreline near shallow mudflat This mud which was the project site is also affected by ship deposited in the 1800s during the boat and seaplane landing wakes hydraulic mining period is slowly degrading and appears to be approach- The project location allows the experi-ing conditions prior to mining ments to be conducted near an armored
shoreline Native oysters are abundant The San Rafael Bay project location is on the lower rip-rap along the shoreline in a coastal area owned by The Nature and eelgrass test plots have been Conservancy and is subject to the successful on this property over the last mixed semi-diurnal tides typical to San 4 years Both eelgrass and native Francisco Bay The east-southeast oysters have been successfully restored orientation of San Rafael Bay provides nearby at the Marin Rod and Gun Club protection from the easterly summer sea Herring often spawn along this shore-breezes and exposure to the southeast- line and should benefit from restored erly winter storms The Marin Islands subtidal habitat National Wildlife Refuge protects the acute
0 50 100 200 Meters
Substrate Elements at San Rafael Bay Substrate Elements at San Rafael BayCross Section C r o s s S e c t i o n
1 m ~ 250 m
MHHW
MLLW
SF Bay Mudflat Lagoon
~1m~1m
1m
Layer cake
Schematic representation not to exact scale
Note
1m
Reef ball stack
1m
Reef castle
1m
Reef ball
6
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
s
acute0 100 20050
Meters
Substrate Elements at Hayward Shoreline NorthC r o s s S e c t i o n
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
MHHW
MLLW
Mudflat
~ 250 m1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound+ eelgrass
Eelgrass Shell bag mound Layer cake Reef castle Reef ballReef ball stack
1m 1m
8
Highest priority To achieve if possible
Appropriate region and depth for eelgrass and oysters
Large enough shoreline oriented so that treatment array can be placed parallel to the shore and perpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison of treatment effects in different regions
Appropriate sediment for oyster reefs and eelgrass
Distance to shore amenable to shore access for ease of monitoring
Same experimental design and depth if mulƟple locaƟons
SoŌ shoreline with paired comparison to hard shoreline nearby if possible
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale Experiment The larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Site Selection Criteria
ELEMENT
UNIT
PLOT
SITE
LOCATION
Project Components
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with
reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
Substrate Experiment The substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Very important
Willing landowners with expected reasonable Ɵme frame for permits approvals
5
DetailLarger scale experiment32 m x 10 m
Proposed Array of Treatments at San Rafael BayP h a s e 1
DetailSubstrate experiment30 m x 1 m
7
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
SF Bay
Lagoon
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Mudflat
Shell bag mounds
Eelgrass vegetative shoots
2 m2 m
1 m1 m
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
S
San Rafael Canal
Location 1 San Rafael Bay
San Rafael Bay lies between Point San site from direct wave action from the Quentin to the south and Point San east out of the more exposed portions Su ments
Tre tsPedro to the north and is a wide of San Pablo Bay The shoreline near shallow mudflat This mud which was the project site is also affected by ship deposited in the 1800s during the boat and seaplane landing wakes hydraulic mining period is slowly degrading and appears to be approach- The project location allows the experi-ing conditions prior to mining ments to be conducted near an armored
shoreline Native oysters are abundant The San Rafael Bay project location is on the lower rip-rap along the shoreline in a coastal area owned by The Nature and eelgrass test plots have been Conservancy and is subject to the successful on this property over the last mixed semi-diurnal tides typical to San 4 years Both eelgrass and native Francisco Bay The east-southeast oysters have been successfully restored orientation of San Rafael Bay provides nearby at the Marin Rod and Gun Club protection from the easterly summer sea Herring often spawn along this shore-breezes and exposure to the southeast- line and should benefit from restored erly winter storms The Marin Islands subtidal habitat National Wildlife Refuge protects the acute
0 50 100 200 Meters
Substrate Elements at San Rafael Bay Substrate Elements at San Rafael BayCross Section C r o s s S e c t i o n
1 m ~ 250 m
MHHW
MLLW
SF Bay Mudflat Lagoon
~1m~1m
1m
Layer cake
Schematic representation not to exact scale
Note
1m
Reef ball stack
1m
Reef castle
1m
Reef ball
6
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
DetailLarger scale experiment32 m x 10 m
Proposed Array of Treatments at San Rafael BayP h a s e 1
DetailSubstrate experiment30 m x 1 m
7
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
SF Bay
Lagoon
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Mudflat
Shell bag mounds
Eelgrass vegetative shoots
2 m2 m
1 m1 m
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
S
San Rafael Canal
Location 1 San Rafael Bay
San Rafael Bay lies between Point San site from direct wave action from the Quentin to the south and Point San east out of the more exposed portions Su ments
Tre tsPedro to the north and is a wide of San Pablo Bay The shoreline near shallow mudflat This mud which was the project site is also affected by ship deposited in the 1800s during the boat and seaplane landing wakes hydraulic mining period is slowly degrading and appears to be approach- The project location allows the experi-ing conditions prior to mining ments to be conducted near an armored
shoreline Native oysters are abundant The San Rafael Bay project location is on the lower rip-rap along the shoreline in a coastal area owned by The Nature and eelgrass test plots have been Conservancy and is subject to the successful on this property over the last mixed semi-diurnal tides typical to San 4 years Both eelgrass and native Francisco Bay The east-southeast oysters have been successfully restored orientation of San Rafael Bay provides nearby at the Marin Rod and Gun Club protection from the easterly summer sea Herring often spawn along this shore-breezes and exposure to the southeast- line and should benefit from restored erly winter storms The Marin Islands subtidal habitat National Wildlife Refuge protects the acute
0 50 100 200 Meters
Substrate Elements at San Rafael Bay Substrate Elements at San Rafael BayCross Section C r o s s S e c t i o n
1 m ~ 250 m
MHHW
MLLW
SF Bay Mudflat Lagoon
~1m~1m
1m
Layer cake
Schematic representation not to exact scale
Note
1m
Reef ball stack
1m
Reef castle
1m
Reef ball
6
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
Su mentsTre ts
S
acute0 100 20050
Meters
6
Location 1 San Rafael Bay
San Rafael Bay lies between Point San Quentin to the south and Point San Pedro to the north and is a wide shallow mudflat This mud which was deposited in the 1800s during the hydraulic mining period is slowly degrading and appears to be approach-ing conditions prior to mining
The San Rafael Bay project location is in a coastal area owned by The Nature Conservancy and is subject to the mixed semi-diurnal tides typical to San Francisco Bay The east-southeast orientation of San Rafael Bay provides protection from the easterly summer sea breezes and exposure to the southeast-erly winter storms The Marin Islands National Wildlife Refuge protects the
site from direct wave action from the east out of the more exposed portions of San Pablo Bay The shoreline near the project site is also affected by ship boat and seaplane landing wakes
The project location allows the experi-ments to be conducted near an armored shoreline Native oysters are abundant on the lower rip-rap along the shoreline and eelgrass test plots have been successful on this property over the last 4 years Both eelgrass and native oysters have been successfully restored nearby at the Marin Rod and Gun Club Herring often spawn along this shore-line and should benefit from restored subtidal habitat
San Rafael Canal
MHHW
MLLW
Mudflat
~ 250 m1 m
LagoonSF Bay
1m 1m 1m 1m
Substrate Elements at San Rafael BayCross Section
Layer cake Reef castle Reef ballReef ball stack
Schematic representation not to exact scale
Note
~1m~1m
Substrate Elements at San Rafael BayC r o s s S e c t i o n
Shell bag mound
Shell bag mound + eelgrass
Eelgrass
~250m
Control
Layer cake
Reef ball stack
1m
1m
Reef castle
Reef ball
San Rafael Bay Location Experiment Details
At this location both the larger scale and substrate experiments will be conducted The substrate experiments will be set up in the 30-m spaces between and on either side of the line of the larger scale plots The four oyster substrate types not tested in the larger scale experiment (reef balls reef castles mini-reef balls layer cakes) will be replicated 5 times for a total of 20 elements These elements will be placed in blocks of four with each of the four substrate types represented once in each block
Proposed Array of Treatments at San Rafael Bay P h a s e 1
Lagoon
Mudflat SF Bay
Detail Larger scale experiment32 m x 10 m
Eelgrass vegetative shoots
Shell bag mounds
Detail Substrate experiment30 m x 1 m
1 m 1 m
2 m 2 m
7
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
ELEMENT
UNIT
PLOT
SITE
LOCATION
5
Experiment Descriptions The project is composed of two types of experiments ldquoLarger scalerdquo experiments to test biological and physical effects of treatment plots and smaller ldquosubstraterdquo experi-ments to test the biological effects of different substrates or surfaces that could be used on a larger scale in future projects
Larger Scale ExperimentThe larger scale experiment will compare the effects of one type of native oyster substrate (oyster shell bags) eelgrass and a combination of the two This experiment will be large enough to examine effects on physical processes such as wave attenuation and sediment accretion as well as effects on biological activities (eg bird and fish utilization water quality interac-tions of oysters and eelgrass) Four large treatment plots (32 meter x 10 meter each) will be situated along a line parallel to and approximately 250 meters from the shore The four plots will each have their own treatment an oyster shell bag treatment an eelgrass treatment a treatment with both oyster shell bags and eelgrass and a control plot with no treatment Oyster units will be separated by 2 meters to minimize scour potential In the combined eelgrass-oyster treatments eelgrass will be added to the oyster arrangement creating a denser treatment plot
Substrate ExperimentThe substrate experiment will compare native oyster recruit-ment and growth for different oyster substrates to inform future restoration projects Single oyster substrate elements (1 meter x 1 meter each) of different types will be lined up parallel to the shoreline with 4 or 5 meter spacing depend-ing on the project site The emphasis is on the biological response in this smaller-scale experiment
Highest priority Very important To achieve if possible
Appropriate region and depth foreelgrass and oysters
Large enough shoreline oriented so that treatment array can be placedparallel to the shore andperpendicular to the direcƟon ofwaves
MulƟple locaƟons to provide replicaƟon and allow comparison oftreatment effects in differentregions
Appropriate sediment for oysterreefs and eelgrass
Distance to shore amenable toshore access for ease of monitoring
Same experimental design anddepth if mulƟple locaƟons
SoŌ shoreline with pairedcomparison to hard shorelinenearby if possible
Project Components
Site Selection Criteria
ELEMENT = 1 X 1 m square of eelgrass shellbag mound with reefball castle or layercake
UNIT = 2 m x 2 m of 4 elements
PLOT = 32 m x 10 m arrangements of units and space between units
LOCATION = place where experiment is conducted either San Rafael Bay or Hayward Shoreline
SITE = arrangement of four plots parallel to shore may contain both large scale and substrate element experiments
Willing landowners with expectedreasonable Ɵme frame for permitsapprovals
Location 2 Hayward Shoreline
The South Bay is a large shallow basin with an inundated deep relict river chan-nel surrounded by broad shallow mudflats small areas of fringing tidal marsh and expansive shoreline armoring The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water leaving an expanse of exposed mudflats Over the past 150 years the subtidal and intertidal flats along the east shore of the South Bay have eroded feeding depositional areas elsewhere across the estuary
The Hayward Shoreline project location is near the eastern shore of South San Fran-cisco Bay near the San Mateo Bridge where it is subject to mixed semi-diurnal tides and open to prevailing winds and waves The intertidal flats are considered ldquosovereign landrdquo held in public trust by the California
s
acute 0 1 00 20050
Meters
Wildlife Conservation Board The project location is adjacent to the Eden Landing Ecological Reserve (ELER) a 6000 acre pond complex that includes Old Alameda Creek Mt Eden Creek North Creek and the Alameda Creek Flood Control Channel
North of Mount Eden Creek the shoreline is riprapped while to the south Whalersquos Tail Marsh provides a softer adjacent marsh edge Native oysters have been found on limited hard substrate in the area and eelgrass grows nearby This location is a shallow mudflat that extends bayward for more than a mile and the depth from shore is a bit shallower than might be ideal for native oysters and eelgrass Thus a phased approach is planned that will permit understanding more about this sitersquos potential before deploying the larger scale treatment plots in a future phase
Substrate Elements at Hayward Shoreline North C r o s s S e c t i o n
MHHW
MLLW
Mudflat
~ 250 m 1 m
Pond E10SF Bay
1m
~1m
1m 1m 1m2m
Shell bag mound + eelgrass
Eelgrass Shell bag moundLayer cake Reef castle Reef ballReef ball stack
1m 1m
8
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
4
The Project Elements
Eelgrass UnitsEelgrass will be planted and seeded in 15 x 15 meter units In each unit 25 plants will be added as whole shoot trans-plants using a bamboo stake planting technique Buoy-deployed seeding will supple-ment transplants and increase genetic diversity flowering shoots of eelgrass will be placed into mesh bags attached to buoys and ripe seeds will then drop onto the restoration site
Oyster Substrate UnitsEach oyster substrate unit will consist of four 1 x 1 meter elements for an overall footprint of 4 m2 Mounds of bagged oyster shell are the primary substrate to be used In addition several other substrates will be tested on a smaller scale
Shell Bag MoundsBags of Pacific oyster shell have been successful in recruit-ing native oysters in several locations in San Francisco Bay Shell bags at a restoration site in San Rafael Bay (Marin Rod and Gun Club) remain intact after 7 years and maintain a viable population of oysters other invertebrates and fish The amount of surface area for juvenile oyster settlement and interstitial space in a bag of shells is larger than any other type of oyster substrate known to the oyster culture industry The mesh covering affords some protection from predators while the oysters are small The shell bag mounds will be set on top of coconut fiber coir fabric We expect some settlement to occur which will require additional shell bags to be added over time
The next four methods involve constructing artificial reef elements from a mixture of roughly 80 native bay sediments (sand clay fossilized native oyster shell) and 20
Dome Style Reef BallsReef Balls are in use in San Francisco Bay at two restoration sites the Marin Rod and Gun Club (San Rafael) and Berkeley Marina (north of Cesar Chavez Park) Reef Balls are hollow with an open top that can be capped They are relatively easy to install and remove and have been demon-strated to be successful in recruit-ing oysters
Reef Ball StacksReef Ball Stacks which combine smaller basketball-sized Reef Balls in a stacked configuration create different sizes of interstitial spaces where oysters can grow The domes are anchored to one another for stability and have the advantages of the single dome-style Reef Ball but are easier to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Layer CakesThe Layer Cake design includes cross-sectional layers from a reef ball mold and mimics naturally occurring rock structure The amount of interstitial space is relatively large particularly under-neath the layer levels These struc-tures are easy to deploy and monitor The project will test this type of structure for the first time in San Francisco Bay
Reef CastlesReef castles are structures built to any dimension as an assortment of vertical and horizontal surfaces They are relatively inexpensive and easy to assemble Reef castles have less three-dimensional surface area than shell bags but are more com-plex than other reef designs which may enhance oyster recruitment by providing more intersti-tial space The project will test this type of structure for the first time in San Francisco Bay
cement These oyster substrates will also be placed onto coir fabric This design should reduce settlement into the sediment and scour around the treatments experienced in previous projects
Buoy-deployed seedingof eelgrass
Eelgrass shootstransplants
Shell bag mound + eelgrass Shell bag mound Eelgrass
Control
~250 m
Shell bag mound + eelgrass Shell bag mound
Eelgrass
Control
~250 m
Hayward Shoreline Location Experiment Details
The project will occur in two phases at the Hayward site Phase 1 will consist of the substrate experiment only to evaluate recruitment of native oysters eelgrass and their associated communities and assess the stability of the heavier oyster elements All five oyster substrate types will be tested as well as an eelgrass-only treatment and an eelgrass-shell bag mound combination all replicated five times This phase will be north of the Mt Eden Creek mouth along the hard shoreline
Levee Pond E10
Hayward Shoreline Mudflat North
Pending the successful outcome of Phase 1 (planned for summer 2012) and adapting the experiment design as necessary the larger scale experiment would be installed in Phase 2 (planned for summer 2013) Phase 2 would be placed north and south of Mt Eden Creek along both the hard and soft shorelines
Proposed Array of Treatments at Hayward Shoreline
to Mt Eden Creek
SF Bay
Phase 2 detail Larger scale experiment 32 m x 10 m Shell bag mound + eelgrass
1m Shell bag mounds
4m Eelgrass vegetative shoots
Layer cake
Reef ball stack
Phase 1 detail Eelgrass
Substrate experiment 40 m x 1 m
Shell bag mound
Reef castle
2 m
1 m
2 m
1 m
Shell bag mound + eelgrass
Reef ball to Mt Eden Creek
Hayward Shoreline Mudflat
Whalersquos Tail Marsh (North)
(ELER)
South
SF Bay
9
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
To create biologically rich and diverse subtidal and low intertidal habitats including eelgrass and oyster reefs as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions
1 Use a pilot-scale experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay2 Compare the effectiveness of different restoration treatments in establishing these habitat-forming species3 Determine the extent to which restoration treatments enhance habitat for invertebrates fish and birds relative to areas lacking structure and pre-treatment conditions4 Determine if the type of treatment (eg oyster reefs eelgrass plantings or combinations of oyster reefs and eelgrass) influences habitat for other species (eg fish) differently 5 Begin to evaluate potential for subtidal restoration to enhance functioning of nearby intertidal mudflat creek and marsh habitats eg by providing food resources to species that move among habitats6 Evaluate potential for living subtidal features to reduce water flow velocities attenuate waves and prevent erosion and assess whether different restoration treatments influence physical processes differently7 Determine if position in the Bay and the specific environmental context at that location influences foundational species establishment habitat provision and physical processes conferred by restoration treatments8 Where possible compare the ability to establish restoration treatments habitat functions and physical changes along mudflatswetlands versus armored shores
3
Living Shorelines in San Francisco Bay
While not a new concept Living Shoreline projects are new to San Francisco Bay where pilot restoration work on eelgrass and oyster reefs began in 2004 Several small-scale subtidal eelgrass restoration projects were established coupled with extensive monitoring and genetics analysis from seven eelgrass beds in the bay Native oyster monitor-ing and restoration efforts produced population data for more than 80 intertidal sites and data on substrate (surface) preferences Successful restoration of tens of thousands of oyster recruits has occurred
The San Francisco Bay Living Shorelines Nearshore Linkages Project builds upon the successful methods and planning from earlier efforts to integrate oyster and eelgrass habitats Resolutions to the constraints timing and design issues encountered in previous efforts have been merged with recommended regional initiatives to create uniquely designed San Francisco Bay Living Shorelines
Overarching Project Goal
Objectives to Achieve Goal
_
_
acute6 0 63 km
_ Hayward Shoreline Site
_ San Rafael Bay Site
Native OystersEelgrass
Potential Impacts Monitoring The small amount of disturbed habitat and the habitat-promoting nature of the project make it unlikely to adversely affect endangered and threatened species Since the project is located offshore no adverse impacts are expected for non-aquatic species Also by design recreational use of the bay near the project locations is not anticipated to be affected
San Francisco Bay and its freshwater tributaries are home to a number of endangered and threatened fish including species of steelheads smelts and salmon Construction activities are not expected to adversely affect these species at either project location Waterbirds and shorebirds will be able to avoid construction crew and boats Marine mammals may forage in the project location but there are no haul-out sites nearby During construction the seabed will be tempo-rarily disturbed which may impact benthic habitats How-ever once installed the oyster elements and eelgrass plant-ings will allow for a more diverse habitat and support the colonization of native oysters eelgrass and myriad other organisms Any impacts from monitoring will be small and temporary Nearby mudflat habitat is abundant so shorebirds will not have to move far to forage while the team members are monitoring Fish traps which have been used for similar research in San Francisco Bay are not expected to trap endangered species Monitoring physical processes will have little if any impact on the biota
Before the project begins bathymetric surveys are planned to establish baseline conditions Other pre-project monitor-ing will include collecting sediment cores to assess benthic invertebrate species richness and density and observing bird fish and epibenthic invertebrate use of the site before construction activities occur
After the experiments have started biological monitoring of eelgrass and oysters will track growth rates densities and recruitment in the different treatments Traps suction sampling and coring will be used to assess fish and inverte-brate responses while waterbird and shorebird densities and behaviors will be tracked The physical processes monitoring will focus on changes to waves currents and sedimentationerosion rates at the larger scale experiment treatments only Water properties will also be measured including temperature salinity pH dissolved oxygen and turbidity
Success Criteria The larger scale project and substrate experiment projects are expected to provide lasting habitat for numerous organisms in the high subtidal to low intertidal zone Natural interannual cycles will cause variation in densities of desired organisms but the project will be deemed successful if one or more of the following criteria are met within the 5-year period following construction
-Native oysters will recruit with densities of gt10000 oysters per acre of substrate -Invertebrate species richness will increase by 15 relative to control plots with no physical structure and initial cores collected prior to construction - The number of visits by fish species to the larger scale project will increase by
50 relative to pre-construction visits and the large control area with no physical structure -Eelgrass will establish and spread to at least twice initial planting densities
10
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
2
Ecological Engineers Eelgrass and Native Oysters
Connecting the PiecesSan Francisco Bay Subtidal Habitat Goals
EelgrassEelgrass is a foundation species that support diverse com-munities of invertebrates fishes and waterfowl and provides attachment locations for algae and encrusting invertebrates Eelgrass is the most widely distributed seagrass in the Northern Hemisphere and occurs along the Pacific Coast of North America from the Bering Strait to lower Baja California An estimated 3400 km2 of seagrass
have been lost globally between 1879 and 2006 largely due to human activities The risk to vital habitat has generated much interest in slowing or reversing this trend In the soft sediments of San Francisco Bay eelgrass provides valuable ecological services yet eelgrass beds cover less than 4000 acres or approximately 1 of submerged land in the bay 12 Biophysical models estimate that nearly 30000 acres of bottom area in San Francisco Bay may be suitable habitat3
The 2010 San Francisco Bay Subtidal Habitat Goals Report (see wwwsfbaysubtidalorg) recommends that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna In addition the South Bay Salt Pond Restoration Project includes multiple wetland restoration sites and project leaders have expressed interest in the potential to integrate deeper habitats into the matrix of newly restored areas
Native OystersNative oysters by attaching to hard substrates form beds that increase living space for many other species thus promoting increased diversity and providing food for fishes and other inverte-brates Historically native Olympia oysters were an abundant and ecologically impor-tant part of the fauna and fishery in West Coast estuaries45 The popularity of the fishery that began in the 1850s and other habitat impacts resulted in the collapse of native oyster populations along the West Coast of the US during the late 19th and early 20th centuries The fishery was lost as were the key ecosys-tem services provided by native oysters
Science Goals Restorat ion Goals
1 Understand the ecosystem services supported by marsh subtidal integration and living shorelines and in what quantities2 Develop best practices for integrating subtidal restoration with adjacent wetlands3 Develop best practices for pilot projects to create living shorelines
1 Explore the integration of upland intertidal and subtidal habitats in San Francisco Bay2 Integrate habitat flexibility to increase resilience in the face of long-term change at habitat restoration sites around the bay3 Explore the use of living shoreline projects as a way to achieve multiple benefits in the future
San Francisco Bay Subtidal Habitat Goals for Subtidal-Wetland Design Integration
The project is being managed by the State Coastal Conser-vancy in collaboration with funding partners including the Environmental Protection Agency San Francisco Estuary Partnership Wildlife Conservation Board and NOAA Fisheries Consultants leading the project include San Francisco State University UC Davis USGS Western Ecological Research Center ESA PWA ENVIRON and Isla Arena Consulting
PartnersPermitting
The State Coastal Conservancy looked to other restoration
efforts for guidance about regulatory overview to bring
Living Shorelines to San Francisco Bay Project managers
used a Joint Aquatic Resource Permit Application (JARPA)
to engage several federal and state agencies simultane-
ously Questions regarding bay fill impacts to existing
wetlands interference with navigation and public access
and notices were addressed during the consultation
process
Regulatory agencies for this project include the San
Francisco Bay Regional Water Quality Control Board
(RWQCB) US Army Corps of Engineers (Corps) CA Dept
of Fish and Game (DFG) National Marine Fisheries Service
(NMFS) San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC)
11
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12
Living Shorelines and Climate ChangeAdaptation
The San Francisco Bay Living Shorelines Nearshore Linkages Project Restoration efforts in San Francisco Bay will advance in Summer 2012 as the San Francisco Bay Living Shorelines Nearshore Linkages Project is implemented The overarch-ing project goal is to analyze subtidal restoration techniques and restore critical eelgrass and oyster habitat while learning more about the potential physical benefits of biological reefs along the shoreline An interdisciplinary team of scientists will test the effectiveness of restoration techniques on subtidal habitat values and begin to evaluate connectivity between submerged areas and adjacent tidal wetlands and creeks This type of work is new to San Francisco Bay but will build on the lessons learned from other restoration efforts in the estuary and around the nation The pilot project will be conducted in two locations in San Rafael Bay and along the Hayward shoreline Through frequent monitoring information will be generated about how the project can be scaled up to balance shoreline protection environmental impacts and habitat needs
What is a Living ShorelineLiving Shoreline projects use a suite of bank stabilization and habitat restoration techniques to reinforce the shore-line minimize coastal erosion and maintain coastal processes while protecting restoring enhancing and creating natural habitat for fish and aquatic plants and wildlife (NOAA Restoration Center) The term ldquoLiving Shorelinesrdquo was coined because the approach provides living space for estuarine and coastal organisms Strategic placement
of native vegetation natural materials and reinforcing rock or shell for native shellfish settlement enhance habitat values by creating new living space The techniques also increase connectivity of wetlands and deeper intertidal and subtidal lands while providing a measure of shoreline protection The approach has been implemented primarily on the East and Gulf Coasts such as in the Chesapeake Bay and along the Alabama-Mississippi coastline
The California Climate Change Adaptation Strategy recommends the use of Living Shorelines as a potential adaptation method to reduce the need for engineered hard shoreline protection devices and to provide habitat functions and values The State Coastal Conservancy Climate Change Policy also recommends Living Shorelines to reduce erosion and trap sediment allowing for buffering of tidal wetlands and migration of habitats Both policies have a goal of improved estuarine habitat resiliency in the future to cope with sea level rise and other environmental changes related to climate change
M A Y 2 0 1 2
Isla Arena C O N S U L T I N G
12
Volunteer Opportunities We welcome community volunteers to participate in monitoring activities with the project Please contact Project Manager Marilyn Latta if you are interested
Contact Us Project Manager Marilyn Latta mlattascccagov 510-286-4157 Science Lead Katharyn Boyer
Timeline
Winter Spring Summer Fal l
Final Design
Permitting
Draft Design
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 1)
Post-deployment Monitoring (Phase 2)
Pre-project Monitoring
Pre-project Monitoring
Project Construction (Phase 2)
Project Construction (Phase 1)
San Rafael Bay
Hayward Shoreline
Project Development
Winter Spring Summer Fal l Winter Spring Summer Fal l
2011 2012 2013
Project Construction (Phase 1)
2017
2017
2017
Literature Cited 1 - Merkel KW and Associates 2003 San Francisco Bay eelgrass inventory Submitted to Caltrans and NOAA Fisheries
2 - Merkel and Associates Inc 2009 San Francisco Bay Eelgrass Atlas Octoberndash November 2009 Submitted to California Department of Transportation and
National Marine Fisheries Service
3 - Merkel and Associates Inc 2004 Baywide eelgrass inventory of San Francisco Bay Pre-survey Screening Model and Eelgrass Survey Report Report to California Department of Transportation
4 - Barrett EM 1963 The California oyster industry CDFG Fishery Bulletin 123 1-103
5 - Baker P 1995 Review of ecology and fishery of the Olympia oyster Ostrealurida with annotated bibliography Journal of Shellfish Research Vol 14 no2 pp 501-518
katboyersfsuedu 415-338-3751
Photo credits Lorenz amp Avelar wwwLorenz-Avelarcom San Francisco State University Romberg-Tiburon Center for Environmental Studies (Wim Kimmerer Katharyn Boyerrsquos lab) Marin Rod and Gun Club and Berkeley Marina native oyster restoration Projects (Robert Abbott Jerry McEwen Rena Obernolte) USGS (Susan de la Cruz) ESA PWA (Doug George)
This document was produced for the State Coastal Conservancy by ESA PWA 2012
Isla Arena C O N S U L T I N G
12